VMD-L Mailing List

From: Ronald Cohen (rcohen_at_carnegiescience.edu)
Date: Fri Aug 02 2024 - 12:07:35 CDT

That’s great. Thank you!

Ron

> On Aug 2, 2024, at 1:06 PM, Diego Gomes <diego.enry_at_gmail.com> wrote:
>
> Hi Ronald,
> I'm writing to confirm the issue of reading cell dimensions while reading the VASP .xml file.
> I'm opening an issue in our GitLab.
>
> By now, I wrote you a script as a workaround. It extracts the cell dimensions from vasprun.xml to a vasprun.xst file.
> You can then into VMD using the pbctools plugin.
>
> # Open the Tk Console
> Extensions->Tk Console
>
> # Read the .xst file.
> pbc readxst vasprun.xst
>
> # Learn more about the PBCTools plugin here.
> https://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/ <https://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/>
>
>
> Friendly,
> Diego.
>
> #
> # Python Script to read "vasprun.xml" and write "vasprun.xst"
> #
> # Import required module
> import xml.etree.ElementTree as ET
>
> # Load/Parse the file
> tree = ET.parse('vasprun.xml')
> root = tree.getroot()
>
> # Initialize a list to hold all basis info
> all_basis_info = []
>
> # Extract basis info for each occurrence of <structure>
> for structure in root.findall(".//structure"):
> basis_info = []
> for v in structure.find(".//varray[@name='basis']"):
> basis_vector = [float(num) for num in v.text.split()]
> basis_info.append(basis_vector)
> all_basis_info.append(basis_info)
>
>
> # Flatten the list of lists using a lambda function
> flatten = lambda lst: [item for sublist in lst for item in sublist]
>
> # Write all basis info to a file
> with open('vasprun.xst', 'w') as output:
> for index, basis in enumerate(all_basis_info):
> flattened_list = flatten(basis)
> xst = ' '.join("{:.4f}".format(num) for num in flattened_list)
> output.write(f'{index+1} {xst}\n')
>
> On Wed, Jul 31, 2024 at 11:24 AM Ronald Cohen <rcohen_at_carnegiescience.edu <mailto:rcohen_at_carnegiescience.edu>> wrote:
> Sure I will be glad to. I have looked at the VASP plugins and all of them assume a fixed cell. Even the atomic positions are thus wrong, because it multiplies the fractional coordinates in the frames by the wrong cell. I just haven't had time to try to modify the plugins myself. It seems there is not a standard form for the plugins, so it is a bit complicated how to do it best. Here are two examples of iron liquid:
>
> https://urldefense.com/v3/__https://www.dropbox.com/scl/fi/e5ydb9lsqddxvh9s8r42v/vasprun.xml.gz?rlkey=zdtmbuo8b5y2epb0jkigqjph2&dl=0__;!!DZ3fjg!-CKXjmdAOOVeEMcfXGasDRJnj2bAo4kWG-QPjqObJyIxUFSZ0PtBsKBKaQGP70p9FZJoZw529jRnyEDHxq-1cX1ljg$ <https://urldefense.com/v3/__https://www.dropbox.com/scl/fi/e5ydb9lsqddxvh9s8r42v/vasprun.xml.gz?rlkey=zdtmbuo8b5y2epb0jkigqjph2&dl=0__;!!DZ3fjg!-CKXjmdAOOVeEMcfXGasDRJnj2bAo4kWG-QPjqObJyIxUFSZ0PtBsKBKaQGP70p9FZJoZw529jRnyEDHxq-1cX1ljg$ >
> https://urldefense.com/v3/__https://www.dropbox.com/scl/fi/ay770hk9kj27egaltew9w/XDATCAR.gz?rlkey=74rdf2plofpbzqkqj975pcax8&dl=0__;!!DZ3fjg!-CKXjmdAOOVeEMcfXGasDRJnj2bAo4kWG-QPjqObJyIxUFSZ0PtBsKBKaQGP70p9FZJoZw529jRnyEDHxq-2ScKsgA$ <https://urldefense.com/v3/__https://www.dropbox.com/scl/fi/ay770hk9kj27egaltew9w/XDATCAR.gz?rlkey=74rdf2plofpbzqkqj975pcax8&dl=0__;!!DZ3fjg!-CKXjmdAOOVeEMcfXGasDRJnj2bAo4kWG-QPjqObJyIxUFSZ0PtBsKBKaQGP70p9FZJoZw529jRnyEDHxq-2ScKsgA$ >
>
>
>
> Sincerely,
>
> Ron
>
>
>> On Jul 31, 2024, at 11:10 AM, Diego Gomes <diego.enry_at_gmail.com <mailto:diego.enry_at_gmail.com>> wrote:
>>
>> Hi Ronald,
>> thank you for bringing this up.
>>
>> Can you send me a sample file and if you know details about the VASP file, a brief explanation of the expected result?
>>
>> Friendly,
>> Diego.
>>
>> --
>> Diego Enry. B. Gomes, PhD
>> Department of Physics at Auburn University &
>> NIH Center for Macromolecular Modeling and Visualization
>> Leach Science Center - Ste. 3182
>> Auburn, AL, 36849 - (334) 844-4264
>> dgomes_at_auburn.edu <mailto:dgomes_at_auburn.edu>
>> On Mon, Jul 29, 2024 at 2:58 PM Ronald Cohen <rcohen_at_carnegiescience.edu <mailto:rcohen_at_carnegiescience.edu>> wrote:
>> I have followed up this in the course of the plugins, and not only does vmd not read the cell parameters correctly with a variable cell, but it even reads the atomic positions wrong!
>> It converts them to cartesian coordinates (angstroms) using the cell of the first frame.
>>
>> Ronald Cohen
>>
>>
>>
>>
>> --
>> Diego Enry B. Gomes, PhD
>> Department of Physics at Auburn University &
>> NIH Center for Macromolecular Modeling and Visualization
>> Leach Science Center - Ste. 3182 - Auburn, AL
>> dgomes_at_auburn.edu <mailto:dgomes_at_auburn.edu>
>
>
>
> --
> Diego Enry B. Gomes, PhD
> Department of Physics at Auburn University &
> NIH Center for Macromolecular Modeling and Visualization
> Leach Science Center - Ste. 3182 - Auburn, AL
> dgomes_at_auburn.edu <mailto:dgomes_at_auburn.edu>